1F8Y

CRYSTAL STRUCTURE ANALYSIS OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE COMPLEXED WITH 5-METHYL-2'-DEOXYPSEUDOURIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of nucleoside 2-deoxyribosyltransferase in native and ligand-bound forms reveal architecture of the active site.

Armstrong, S.R.Cook, W.J.Short, S.A.Ealick, S.E.

(1996) Structure 4: 97-107

  • Primary Citation of Related Structures:  1F8X

  • PubMed Abstract: 
  • Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an ac ...

    Nucleoside 2-deoxyribosyltransferase plays an important role in the salvage pathway of nucleotide metabolism in certain organisms, catalyzing the cleavage of beta-2'-deoxyribonucleosides and the subsequent transfer of the deoxyribosyl moiety to an acceptor purine or pyrimidine base. The kinetics describe a ping-pong-bi-bi pathway involving the formation of a covalent enzyme-deoxyribose intermediate. The enzyme is produced by a limited number of microorganisms and its functions have been exploited in its use as a biocatalyst to synthesize nucleoside analogs of therapeutic interest.


    Organizational Affiliation

    Section of Biochemistry, Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
A, B
157Lactobacillus leichmanniiGene Names: ntd
EC: 2.4.2.6
Find proteins for Q9R5V5 (Lactobacillus leichmannii)
Go to UniProtKB:  Q9R5V5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5MD
Query on 5MD

Download SDF File 
Download CCD File 
A, B
2'-deoxy-1-methyl-pseudouridine
5-METHYL-2'-DEOXYPSEUDOURIDINE
C10 H14 N2 O5
AMDJRICBYOAHBZ-XLPZGREQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.160 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 149.600α = 90.00
b = 149.600β = 90.00
c = 149.600γ = 90.00
Software Package:
Software NamePurpose
SDMSdata scaling
X-PLORphasing
X-PLORrefinement
X-PLORmodel building
SDMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance